I just bought an 02 TJ that the PO had done some upgrades on (Ford 8.8, adjustable upper CAs, SYE & 1.5" transfer case drop) & needed some others (sagging rear springs, old Rancho control arm bushings shot, interference with the diff cover & rear track arm on the gas tank skid plate). It had a bad vibration too. I pulled the rear driveline and had a shop look at it, bad u-joint & rebalanced it. Still had the vibration.
After reading Chris's suggestions, I removed the spacers & replaced the springs with an OME 2.5" set. Vibration is now gone. Driveline/pinion angle is much better, even to the naked eye.
Maybe sharing some pics of your pinion angle would help with suggestions.